Problem with Boolean-difference modifier – or – How to model a cuboid with two cylindric holes
Because an intersection between two cylinders at 90 degrees is a 45 degree miter, this isn't too hard to model. Z up, Y along the lenght, X across


K with C to constrain and Z to cut through, make 2 45 degree cuts into  a half-cylinder as shown
E (right-click to cancel transform) followed by SX extrude the long edges outwards
Select all the faces, E extrude them downwards, followed by SZ0 about their median point to flatten them.
Select the central hole-faces on both sides, and CtrlE &gt; Bridge Edge Loops
Header select menu &gt; Select Sharp Edges, and add some by hand to complete the circumference of the top hole. Set the Bevel Weight of all the selected edges to 1.00

Assign a Bevel modifier by Weight, Segments 2, Profile 1.00. I usually switch off the clamps, and reduce the width until everything looks correct. Assign a Subdivision Surface modifier.